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Biomedical Sciences - Human Genetics | Molecular Methods for Evolutionary Genetics

Molecular Methods for Evolutionary Genetics

Series: Methods in Molecular Biology, Vol. 772

Orgogozo, Virginie, Rockman, Matthew V. (Eds.)

2011, XVI, 503p. 81 illus., 4 illus. in color.

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

We are entering a particularly fruitful period in evolutionary genetics, as rapid technological progress transforms the investigation of genetic variation within and between species. Molecular Methods for Evolutionary Genetics is a collection of advanced molecular biology protocols and general overviews intended to represent the essential methods currently bringing evolutionary genetics to fruition. Divided into six thematic sections, this volume covers methods for characterizing genomes, diverse approaches to enrich DNA for subsets of the genome prior to sequencing, and state-of-the-art protocols for sampling genetic variation for genetic mapping studies and population genetic studies (RAD sequencing, Sequenom, microarrays, etc.). The volume concludes by focusing on methods to study candidate genes, from obtaining their sequences and analyzing their transcripts to experimentally manipulating their activities in vivo. Written in the highly successful Methods in Molecular Biology™ series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.


Authoritative and accessible, Molecular Methods for Evolutionary Genetics serves as a rich resource to biologists interested in evolution, whether they be specialists or beginners in molecular biology.

Content Level » Professional/practitioner

Keywords » PCR - fosmid genomic libraries - mRNA - microarray - phenotypic evolution - transcriptome

Related subjects » Human Genetics

Table of contents 

Part I. Characterizing the Genome


1. Genome Size Determination using Flow Cytometry of Propidium Iodide-stained Nuclei

            Emily E. Hare and J. Spencer Johnston


2. Chromosome Analysis in Invertebrates and Vertebrates

            David M. Rowell, Shu Ly Lim and Frank Grutzner


3. Genomic Libraries. I. Construction and Screening of Fosmid Genomic Libraries

            Mike A. Quail, Lucy Matthews, Sarah Sims, Christine Lloyd, Helen Beasley, and Simon W. Baxter


4. Genomic Libraries. II. Subcloning, Sequencing, and Assembling Large-insert Genomic DNA Clones

            Mike A. Quail, Lucy Matthews, Sarah Sims, Christine Lloyd, Helen Beasley, and Simon W. Baxter



Part II. Targeting Regions of the Genome


5. Reduced Representation Methods for Sub-genomic Enrichment and Next-generation Sequencing

            Jeffrey M. Good


6. Accessing the Transcriptome: How to Normalize mRNA Pools

            Heiko Vogel and Christopher W. Wheat


7. Transcriptome Sequencing Goals, Assembly, and Assessment

            Christopher W. Wheat and Heiko Vogel


8. Rapid Retrieval of DNA Target Sequences by Primer Extension Capture

            Adrian W. Briggs


Part III. Measuring Genetic Diversity


9. SNP Discovery and Genotyping for Evolutionary Genetics using RAD Sequencing

            Paul D. Etter, Susan Bassham, Paul A. Hohenlohe, Eric Johnson, and William A. Cresko


10. DNA Microarray-based Mutation Discovery and Genotyping

            David Gresham


11. Genotyping with Sequenom

            Martina Bradić, João Costa, and Ivo M. Chelo


12. Isolating Microsatellite Loci: Looking Back, Looking Ahead

            José A. Andrés and Steven M. Bogdanowicz


13. Design of Custom Oligonucleotide Microarrays for Single Species or Interspecies Hybrids using Array Oligo Selector

            Amy A. Caudy


Part IV. Obtaining Candidate Gene Sequences

14. Identification of Homologous Gene Sequences by PCR with Degenerate Primers

            Michael Lang and Virginie Orgogozo


15. Characterizing cDNA Ends by Circular RACE

            Patrick T. McGrath


16. Identification of DNA Sequences that Flank a Known Region by Inverse PCR

            Anastasios Pavlopoulos


Part V. Analyzing Candidate Gene Transcripts

17. Quantification of Transcript Levels with Quantitative RT-PCR

            Karen L. Carleton


18. Using Pyrosequencing to Measure Allele-specific mRNA Abundance and Infer the Effects of Cis- and Trans-regulatory Differences

            Patricia J. Wittkopp


19. Whole Mount In situ Hybridization of Sectioned Tissues of Species Hybrids to Detect Cis-Regulatory Changes in Gene Expression Pattern

            Ryo Futahashi


20. Identifying Fluorescently Labeled Single Molecules in Image Stacks using Machine Learning            

            Scott Rifkin


Part VI. Testing Candidate Genes and Candidate Mutations


21. Experimental Approaches to Evaluate the Contributions of Candidate Cis-regulatory Mutations to Phenotypic Evolution

            Mark Rebeiz and Thomas M. Williams


22. Experimental Approaches to Evaluate the Contributions of Candidate Protein-coding Mutations to Phenotypic Evolution

            Jay F. Storz and Anthony J. Zera


23. Making Reporter Gene Constructs to Analyze Cis-regulatory Elements

            José Bessa and José Luis Gómez-Skarmeta


24. PCR-directed In vivo Plasmid Construction using Homologous Recombination in Baker’s Yeast

            Erik C. Andersen


25. Production of Fosmid Genomic Libraries Optimized for Liquid Culture Recombineering and Cross-species Transgensis

            Radoslaw Kamil Ejsmont, Maria Bogdanzaliewa, Kamil Andrzej Lipinski, and Pavel Tomancak


26. Recombination-mediated Genetic Engineering of Large Genomic DNA Transgenes

            Radoslaw Kamil Ejsmont, Peter Ahlfeld, Andrei Pozniakovsky, A. Francis Steward, Pavel Tomancak, and Mihail Sarov


27. Overlap Extension PCR: An Efficient Method for Transgene Construction

            Matthew D. Nelson and David H. A. Fitch


28. Gene Knockdown Analysis by Double-stranded RNA Injection
            Benjamin N. Philip and Yoshinori Tomoyasu

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